Bio::SearchIO::XML BlastHandler
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Summary
Bio::SearchIO::XML::BlastHandler - XML Handler for NCBI Blast XML parsing.
Package variables
Privates (from "my" definitions)
%MODEMAP = ( 'Iteration' => 'result', 'Hit' => 'hit', 'Hsp' => 'hsp')
%MAPPING = ( 'BlastOutput_program' => 'RESULT-algorithm_name', 'BlastOutput_version' => 'RESULT-algorithm_version', 'BlastOutput_db' => 'RESULT-database_name', 'BlastOutput_reference' => 'RESULT-program_reference', 'BlastOutput_query-def' => 'RESULT-query_description', 'BlastOutput_query-len' => 'RESULT-query_length', 'BlastOutput_query-ID' => 'runid', 'Parameters_matrix' => { 'RESULT-parameters' => 'matrix'}, 'Parameters_expect' => { 'RESULT-parameters' => 'expect'}, 'Parameters_include' => { 'RESULT-parameters' => 'include'}, 'Parameters_sc-match' => { 'RESULT-parameters' => 'match'}, 'Parameters_sc-mismatch' => { 'RESULT-parameters' => 'mismatch'}, 'Parameters_gap-open' => { 'RESULT-parameters' => 'gapopen'}, 'Parameters_gap-extend' => { 'RESULT-parameters' => 'gapext'}, 'Parameters_filter' => {'RESULT-parameters' => 'filter'}, 'Statistics_db-num' => 'RESULT-database_entries', 'Statistics_db-len' => 'RESULT-database_letters', 'Statistics_hsp-len' => { 'RESULT-statistics' => 'hsplength'}, 'Statistics_eff-space' => { 'RESULT-statistics' => 'effectivespace'}, 'Statistics_kappa' => { 'RESULT-statistics' => 'kappa' }, 'Statistics_lambda' => { 'RESULT-statistics' => 'lambda' }, 'Statistics_entropy' => { 'RESULT-statistics' => 'entropy'}, 'Hsp_bit-score' => 'HSP-bits', 'Hsp_score' => 'HSP-score', 'Hsp_evalue' => 'HSP-evalue', 'Hsp_query-from' => 'HSP-query_start', 'Hsp_query-to' => 'HSP-query_end', 'Hsp_hit-from' => 'HSP-hit_start', 'Hsp_hit-to' => 'HSP-hit_end', 'Hsp_positive' => 'HSP-conserved', 'Hsp_identity' => 'HSP-identical', 'Hsp_gaps' => 'HSP-gaps', 'Hsp_hitgaps' => 'HSP-hit_gaps', 'Hsp_querygaps' => 'HSP-query_gaps', 'Hsp_qseq' => 'HSP-query_seq', 'Hsp_hseq' => 'HSP-hit_seq', 'Hsp_midline' => 'HSP-homology_seq', 'Hsp_align-len' => 'HSP-hsp_length', 'Hsp_query-frame'=> 'HSP-query_frame', 'Hsp_hit-frame' => 'HSP-hit_frame', 'Hit_id' => 'HIT-name', 'Hit_len' => 'HIT-length', 'Hit_accession' => 'HIT-accession', 'Hit_def' => 'HIT-description', 'Hit_num' => 'HIT-order', 'Iteration_iter-num' => 'HIT-iteration', 'Iteration_stat' => 'HIT-iteration_statistic', 'Iteration_query-def' => 'RESULT-query_description', 'Iteration_query-len' => 'RESULT-query_length', 'Iteration_query-ID' => 'runid', )
%IGNOREDTAGS = ( 'Hsp_num' => 1, 'Hsp_pattern-from' => 1, 'Hsp_pattern-to' => 1, 'Hsp_density' => 1, 'Iteration_message' => 1, 'Hit_hsps' => 1, 'BlastOutput_param' => 1, 'Iteration_hits' => 1, 'Statistics' => 1, 'Parameters' => 1, 'BlastOutput' => 1, 'BlastOutput_iterations' => 1, )
Inherit
Bio::Root::Root XML::SAX::Base
Synopsis
  # This is not to be used directly.
Description
This is the XML handler for BLAST XML parsing. Currently it passes elements off
to the event handler, which is ultimately responsible for Bio::Search object
generation.
This was recently split off from the original code for Bio::SearchIO::blastxml
primarily for maintenance purposes.
Methods
start_documentDescriptionCode
end_documentDescriptionCode
start_elementDescriptionCode
end_elementDescriptionCode
charactersDescriptionCode
eventHandler
No description
Code
Methods description
start_documentcode    nextTop
 Title   : start_document
 Usage   : $parser->start_document;
 Function: SAX method to indicate starting to parse a new document
 Returns : none
 Args    : none
end_documentcodeprevnextTop
 Title   : end_document
 Usage   : $parser->end_document;
 Function: SAX method to indicate finishing parsing a new document
 Returns : Bio::Search::Result::ResultI object
 Args    : none
start_elementcodeprevnextTop
 Title   : start_element
 Usage   : $parser->start_element($data)
 Function: SAX method to indicate starting a new element
 Returns : none
 Args    : hash ref for data
end_elementcodeprevnextTop
 Title   : end_element
 Usage   : $parser->end_element($data)
 Function: Signals finishing an element
 Returns : Bio::Search object dpending on what type of element
 Args    : hash ref for data
characterscodeprevnextTop
 Title   : characters
 Usage   : $parser->characters($data)
 Function: Signals new characters to be processed
 Returns : characters read
 Args    : hash ref with the key 'Data'
Methods code
start_documentdescriptionprevnextTop
sub start_document {
    my ($self) = @_;
    $self->{'_lasttype'} = '';
    $self->{'_values'} = {};
    $self->{'_result'}= [];
}
end_documentdescriptionprevnextTop
sub end_document {
   my ($self,@args) = @_;
   
   # reset data carried throughout parse
   $self->{'_resultdata'} = undef;
   
   # pass back ref to results queue; caller must reset handler results queue
   return $self->{'_result'};
}
start_elementdescriptionprevnextTop
sub start_element {
    my ($self,$data) = @_;
    # we currently don't care about attributes
    my $nm = $data->{'Name'};

    if( my $type = $MODEMAP{$nm} ) {
        if( $self->eventHandler->will_handle($type) ) {
            my $func = sprintf("start_%s",lc $type);
            $self->eventHandler->$func($data->{'Attributes'});
        }                                                    
    }
}
end_elementdescriptionprevnextTop
sub end_element {
    my ($self,$data) = @_;

    my $nm = $data->{'Name'};
    my $rc;
    if($nm eq 'BlastOutput_program' &&
       $self->{'_last_data'} =~ /(t?blast[npx])/i ) {
        $self->{'_type'} = uc $1; 
    }
    if ($nm eq 'Iteration') {
        map {
            $self->{'_values'}->{$_} = $self->{'_resultdata'}->{$_};
            } keys %{ $self->{'_resultdata'} };
    }
    if( my $type = $MODEMAP{$nm} ) {
        if( $self->eventHandler->will_handle($type) ) {
            my $func = sprintf("end_%s",lc $type);
            $rc = $self->eventHandler->$func($self->{'_type'},
                                              $self->{'_values'});
        }
    }
    elsif( exists $MAPPING{$nm} ) { 
        if ( ref($MAPPING{$nm}) =~ /hash/i ) {
            my $key = (keys %{$MAPPING{$nm}})[0];
            $self->{'_values'}->{$key}->{$MAPPING{$nm}->{$key}} = $self->{'_last_data'};
        } else {
            $self->{'_values'}->{$MAPPING{$nm}} = $self->{'_last_data'};
        }
    }
    elsif( exists $IGNOREDTAGS{$nm} ){
        # ignores these elements for now
    }
    else {      
        $self->debug("ignoring unrecognized element type $nm\n");
    }
    $self->{'_last_data'} = ''; # remove read data if we are at 
                                # end of an element
                                
    # add to ResultI array
    $self->{'_result'} = $rc if( $nm eq 'Iteration' );
    # reset values for each Result round
    if ($nm eq 'Iteration') {
        $self->{'_values'} = {};
    }
}
charactersdescriptionprevnextTop
sub characters {
   my ($self,$data) = @_;
   return unless ( defined $data->{'Data'} && $data->{'Data'} !~ /^\s+$/ );
   $self->{'_last_data'} .= $data->{'Data'};
}
eventHandlerdescriptionprevnextTop
sub eventHandler {
    my $self = shift;
    return $self->{'_handler'} = shift if @_;
    return $self->{'_handler'};
}

1;
}
General documentation
DEPENDENCIESTop
In addition to parts of the Bio:: hierarchy, this module uses:
 XML::SAX::Base
which comes with the XML::SAX distribution.
FEEDBACKTop
Mailing ListsTop
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
Support Top
Please direct usage questions or support issues to the mailing list:
bioperl-l@bioperl.org
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
Reporting BugsTop
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via the
web:
  https://redmine.open-bio.org/projects/bioperl/
AUTHOR - Jason Stajich, Chris FieldsTop
Email jason-at-bioperl.org
Email cjfields-at-uiuc dot edu
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
SAX methodsTop